X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FColumnSelection.java;h=835d7e97f94ced58f0b00e494684095354ec1f49;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=b7bc40e357df4c798a545cf7c7a01b3d2a4f2976;hpb=10e637daad8983c41db8679baabea5563d7371f4;p=jalview.git

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index b7bc40e..835d7e9 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -25,8 +25,7 @@ import jalview.viewmodel.annotationfilter.AnnotationFilterParameter;
 import jalview.viewmodel.annotationfilter.AnnotationFilterParameter.SearchableAnnotationField;
 
 import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
+import java.util.Collections;
 import java.util.List;
 import java.util.Vector;
 
@@ -35,7 +34,7 @@ import java.util.Vector;
  */
 public class ColumnSelection
 {
-  Vector selected = new Vector();
+  Vector<Integer> selected = new Vector<Integer>();
 
   // Vector of int [] {startCol, endCol}
   Vector<int[]> hiddenColumns;
@@ -64,7 +63,7 @@ public class ColumnSelection
   }
 
   /**
-   * removes col from selection
+   * Removes value 'col' from the selection (not the col'th item)
    * 
    * @param col
    *          index of column to be removed
@@ -75,6 +74,8 @@ public class ColumnSelection
 
     if (selected.contains(colInt))
     {
+      // if this ever changes to List.remove(), ensure Integer not int argument
+      // as List.remove(int i) removes the i'th item which is wrong
       selected.removeElement(colInt);
     }
   }
@@ -131,7 +132,7 @@ public class ColumnSelection
    */
   public int columnAt(int i)
   {
-    return ((Integer) selected.elementAt(i)).intValue();
+    return selected.elementAt(i).intValue();
   }
 
   /**
@@ -201,6 +202,7 @@ public class ColumnSelection
 
       if (temp >= start)
       {
+        // if this ever changes to List.set(), swap parameter order!!
         selected.setElementAt(new Integer(temp - change), i);
       }
     }
@@ -258,6 +260,7 @@ public class ColumnSelection
 
       if (temp >= start)
       {
+        // if this ever changes to List.set(), swap parameter order!!
         selected.setElementAt(new Integer(temp - change), i);
       }
     }
@@ -303,13 +306,13 @@ public class ColumnSelection
   {
     if (shiftrecord != null)
     {
-      Vector shifts = shiftrecord.shifts;
+      final List<int[]> shifts = shiftrecord.getShifts();
       if (shifts != null && shifts.size() > 0)
       {
         int shifted = 0;
         for (int i = 0, j = shifts.size(); i < j; i++)
         {
-          int[] sh = (int[]) shifts.elementAt(i);
+          int[] sh = shifts.get(i);
           // compensateForEdit(shifted+sh[0], sh[1]);
           compensateForDelEdits(shifted + sh[0], sh[1]);
           shifted -= sh[1];
@@ -324,16 +327,17 @@ public class ColumnSelection
    * removes intersection of position,length ranges in deletions from the
    * start,end regions marked in intervals.
    * 
-   * @param deletions
+   * @param shifts
    * @param intervals
    * @return
    */
-  private boolean pruneIntervalVector(Vector deletions, Vector intervals)
+  private boolean pruneIntervalVector(final List<int[]> shifts,
+          Vector<int[]> intervals)
   {
     boolean pruned = false;
-    int i = 0, j = intervals.size() - 1, s = 0, t = deletions.size() - 1;
-    int hr[] = (int[]) intervals.elementAt(i);
-    int sr[] = (int[]) deletions.elementAt(s);
+    int i = 0, j = intervals.size() - 1, s = 0, t = shifts.size() - 1;
+    int hr[] = intervals.elementAt(i);
+    int sr[] = shifts.get(s);
     while (i <= j && s <= t)
     {
       boolean trailinghn = hr[1] >= sr[0];
@@ -341,7 +345,7 @@ public class ColumnSelection
       {
         if (i < j)
         {
-          hr = (int[]) intervals.elementAt(++i);
+          hr = intervals.elementAt(++i);
         }
         else
         {
@@ -354,7 +358,7 @@ public class ColumnSelection
       { // leadinghc disjoint or not a deletion
         if (s < t)
         {
-          sr = (int[]) deletions.elementAt(++s);
+          sr = shifts.get(++s);
         }
         else
         {
@@ -374,7 +378,7 @@ public class ColumnSelection
           j--;
           if (i <= j)
           {
-            hr = (int[]) intervals.elementAt(i);
+            hr = intervals.elementAt(i);
           }
           continue;
         }
@@ -400,7 +404,7 @@ public class ColumnSelection
           // sr contained in hr
           if (s < t)
           {
-            sr = (int[]) deletions.elementAt(++s);
+            sr = shifts.get(++s);
           }
           else
           {
@@ -414,15 +418,16 @@ public class ColumnSelection
     // operations.
   }
 
-  private boolean pruneColumnList(Vector deletion, Vector list)
+  private boolean pruneColumnList(final List<int[]> shifts,
+          Vector<Integer> list)
   {
-    int s = 0, t = deletion.size();
-    int[] sr = (int[]) list.elementAt(s++);
+    int s = 0, t = shifts.size();
+    int[] sr = shifts.get(s++);
     boolean pruned = false;
     int i = 0, j = list.size();
     while (i < j && s <= t)
     {
-      int c = ((Integer) list.elementAt(i++)).intValue();
+      int c = list.elementAt(i++).intValue();
       if (sr[0] <= c)
       {
         if (sr[1] + sr[0] >= c)
@@ -434,7 +439,7 @@ public class ColumnSelection
         {
           if (s < t)
           {
-            sr = (int[]) deletion.elementAt(s);
+            sr = shifts.get(s);
           }
           s++;
         }
@@ -453,7 +458,7 @@ public class ColumnSelection
   {
     if (deletions != null)
     {
-      Vector shifts = deletions.shifts;
+      final List<int[]> shifts = deletions.getShifts();
       if (shifts != null && shifts.size() > 0)
       {
         // delete any intervals intersecting.
@@ -485,8 +490,8 @@ public class ColumnSelection
    */
   public List<int[]> getHiddenColumns()
   {
-    return hiddenColumns == null ? Arrays.asList(new int[]
-    {}) : hiddenColumns;
+    return hiddenColumns == null ? Collections.<int[]> emptyList()
+            : hiddenColumns;
   }
 
   /**
@@ -644,7 +649,7 @@ public class ColumnSelection
   {
     if (hiddenColumns == null)
     {
-      hiddenColumns = new Vector();
+      hiddenColumns = new Vector<int[]>();
     }
 
     boolean added = false;
@@ -780,7 +785,7 @@ public class ColumnSelection
     {
       if (copy.selected != null)
       {
-        selected = new Vector();
+        selected = new Vector<Integer>();
         for (int i = 0, j = copy.selected.size(); i < j; i++)
         {
           selected.addElement(copy.selected.elementAt(i));
@@ -788,7 +793,7 @@ public class ColumnSelection
       }
       if (copy.hiddenColumns != null)
       {
-        hiddenColumns = new Vector(copy.hiddenColumns.size());
+        hiddenColumns = new Vector<int[]>(copy.hiddenColumns.size());
         for (int i = 0, j = copy.hiddenColumns.size(); i < j; i++)
         {
           int[] rh, cp;
@@ -885,7 +890,7 @@ public class ColumnSelection
   {
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
-      Vector visiblecontigs = new Vector();
+      List<int[]> visiblecontigs = new ArrayList<int[]>();
       List<int[]> regions = getHiddenColumns();
 
       int vstart = start;
@@ -904,7 +909,7 @@ public class ColumnSelection
         }
         if (hideStart > vstart)
         {
-          visiblecontigs.addElement(new int[]
+          visiblecontigs.add(new int[]
           { vstart, hideStart - 1 });
         }
         vstart = hideEnd + 1;
@@ -912,18 +917,18 @@ public class ColumnSelection
 
       if (vstart < end)
       {
-        visiblecontigs.addElement(new int[]
+        visiblecontigs.add(new int[]
         { vstart, end - 1 });
       }
       int[] vcontigs = new int[visiblecontigs.size() * 2];
       for (int i = 0, j = visiblecontigs.size(); i < j; i++)
       {
-        int[] vc = (int[]) visiblecontigs.elementAt(i);
-        visiblecontigs.setElementAt(null, i);
+        int[] vc = visiblecontigs.get(i);
+        visiblecontigs.set(i, null);
         vcontigs[i * 2] = vc[0];
         vcontigs[i * 2 + 1] = vc[1];
       }
-      visiblecontigs.removeAllElements();
+      visiblecontigs.clear();
       return vcontigs;
     }
     else
@@ -970,7 +975,7 @@ public class ColumnSelection
     if (hiddenColumns != null && hiddenColumns.size() > 0)
     {
       // then mangle the alignmentAnnotation annotation array
-      Vector annels = new Vector();
+      Vector<Annotation []> annels = new Vector<Annotation []>();
       Annotation[] els = null;
       List<int[]> regions = getHiddenColumns();
       int blockStart = start, blockEnd = end;
@@ -1026,12 +1031,12 @@ public class ColumnSelection
       {
         return;
       }
-      Enumeration e = annels.elements();
+
       alignmentAnnotation.annotations = new Annotation[w];
       w = 0;
-      while (e.hasMoreElements())
+
+        for (Annotation [] chnk : annels)
       {
-        Annotation[] chnk = (Annotation[]) e.nextElement();
         System.arraycopy(chnk, 0, alignmentAnnotation.annotations, w,
                 chnk.length);
         w += chnk.length;
@@ -1079,15 +1084,13 @@ public class ColumnSelection
   {
     if (colsel != null && colsel.size() > 0)
     {
-      Enumeration e = colsel.getSelected().elements();
-      while (e.hasMoreElements())
+      for (Integer col : colsel.getSelected())
       {
-        Object eo = e.nextElement();
-        if (hiddenColumns != null && isVisible(((Integer) eo).intValue()))
+        if (hiddenColumns != null && isVisible(col.intValue()))
         {
-          if (!selected.contains(eo))
+          if (!selected.contains(col))
           {
-            selected.addElement(eo);
+            selected.addElement(col);
           }
         }
       }
@@ -1102,22 +1105,20 @@ public class ColumnSelection
    */
   public void setElementsFrom(ColumnSelection colsel)
   {
-    selected = new Vector();
+    selected = new Vector<Integer>();
     if (colsel.selected != null && colsel.selected.size() > 0)
     {
       if (hiddenColumns != null && hiddenColumns.size() > 0)
       {
         // only select visible columns in this columns selection
-        selected = new Vector();
         addElementsFrom(colsel);
       }
       else
       {
         // add everything regardless
-        Enumeration en = colsel.selected.elements();
-        while (en.hasMoreElements())
+        for (Integer col : colsel.getSelected())
         {
-          selected.addElement(en.nextElement());
+          addElement(col);
         }
       }
     }